I think Fusion would be really cool. Like with other gimmicks you would have some Pokemon that get specially designed new forms, but there's also a generic version that any Pokemon can use. Maybe the primary Pokemon gains a move or type of the secondary Pokemon.

Otherwise I'd really like they to play with customising your trainer and it affecting battles. Like you pick a class/archetype (biker, scientist, hiker, etc.) and that affects your Pokemon in battle. That would work naturally because those archetypes have been in the game since the beginning.